# List of top-scoring protein chains for t04-100-30-bys-scores hidden Markov model. # HMM and HMM E-value scores computed by SAM (c) 1992-2001 Regents of the University of California, Santa Cruz # Sequence Alignment and Modeling Software System # http://www.cse.ucsc.edu/research/compbio/sam.html # ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- # R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: # Extension and analysis of the basic method, CABIOS 12:95-107, 1996. # K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting # remote protein homologies, Bioinformatics 14(10):846-856, 1998. # A. Krogh et al., Hidden Markov models in computational biology: # Applications to protein modeling, JMB 235:1501-1531, Feb 1994. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 1sdjA 310 2.16e-01 d.21.1.2,d.21.1.2 98807,98808 1w61A 414 2.81e-01 1qyaA 307 3.14e-01 d.21.1.2,d.21.1.2 104653,104654 2gkeA 274 3.47e-01 1gqzA 274 3.96e-01 d.21.1.1,d.21.1.1 83311,83312 1bwzA 274 4.30e-01 1bwzA d.21.1.1,d.21.1.1 38337,38338 1lm6A 215 2.08e+00 d.167.1.1 84628 1vhzA 198 2.57e+00 d.113.1.1 100718 1omrA 201 2.85e+00 a.39.1.5 93349 1rec 201 2.85e+00 1rec a.39.1.5 17326 1ux8A 132 3.00e+00 1k3bB 164 3.45e+00 d.3.1.1 72015 1u84A 90 3.59e+00 1ci3M 249 4.89e+00 1hcz b.2.6.1,b.84.2.2 22480,28266 1orrA 347 5.10e+00 c.2.1.2 93460 1v58A 241 5.20e+00 c.47.1.9,d.17.3.1 108371,108372 1mkeA 152 5.37e+00 b.55.1.4 79231 2f6uA 234 5.43e+00 1jjiA 311 6.07e+00 c.69.1.2 66766 1dlwA 116 6.21e+00 1dlyA a.1.1.1 14982 2aieP 203 6.37e+00 1ufbA 127 6.54e+00 a.24.16.3 99331 1xo1A 291 7.60e+00 1exnA a.60.7.1,c.120.1.2 18086,33356 1bupA 386 7.76e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 2g6yA 217 8.06e+00 1kay 381 8.22e+00 1ba1 c.55.1.1,c.55.1.1 33385,33386 1z0mA 96 8.60e+00 1y3nA 490 8.68e+00 1zynA 202 9.08e+00 1l5jA 865 9.31e+00 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 1szwA 379 9.78e+00 d.265.1.4 99047 2f15A 96 9.96e+00 1lj5A 379 1.07e+01 e.1.1.1 73928 1z0nA 96 1.08e+01 1r7lA 110 1.09e+01 d.277.1.1 104837 7fd1A 106 1.12e+01 1a6l d.58.1.2 38953 1wkvA 389 1.12e+01 1vrmA 325 1.13e+01 1cwvA 492 1.15e+01 1cwvA b.1.14.1,b.1.14.1,b.1.14.1,b.1.14.1,d.169.1.3 22373,22374,22375,22376,42442 1ut8A 291 1.16e+01 a.60.7.1,c.120.1.2 99908,99909 1rzl 91 1.27e+01 1rzl a.52.1.1 17817 1ihp 438 1.29e+01 1ihp c.60.1.2 33993 2ckiA 262 1.31e+01 1oc2A 348 1.34e+01 c.2.1.2 92765 1x6zA 123 1.36e+01 1qhkA 47 1.37e+01 1qhkA d.100.1.2 40694 1kepA 348 1.38e+01 c.2.1.2 68536 1ut9A 609 1.38e+01 a.102.1.2,b.1.18.2 99912,99913 1lt3A 240 1.46e+01 1lt3A d.166.1.1 42230 1bqsA 209 1.48e+01 1bqsA b.1.1.4,b.1.1.4 21704,21705 1u2hA 99 1.49e+01 2beiA 170 1.50e+01 1u0kA 288 1.55e+01 d.21.1.2,d.21.1.2 107547,107548 1a48 306 1.63e+01 1a48 d.143.1.1 41590 1y0gA 191 1.63e+01 2sli 679 1.67e+01 2sli b.29.1.9,b.68.1.1 24274,27611 2fz4A 237 1.79e+01 1hyuA 521 1.82e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 4fiv 113 1.83e+01 1fmb b.50.1.1 26762 2b59B 172 1.85e+01 1pylA 97 1.87e+01 d.1.1.2 104391 1g8iA 190 1.91e+01 1rec a.39.1.5 60363 1x99A 145 1.95e+01 2stv 195 1.95e+01 2stv b.121.7.1 23287 1q06A 135 1.95e+01 a.6.1.3 95493 2bukA 196 1.96e+01 2cr4A 126 2.01e+01 1otgA 125 2.02e+01 1otgA d.80.1.2 39831 3fivA 116 2.05e+01 1fmb b.50.1.1 26768 1mqoA 227 2.06e+01 d.157.1.1 103846 1ooyA 481 2.14e+01 c.124.1.3,c.124.1.2 93388,93389 1fe0A 68 2.14e+01 1cc8A d.58.17.1 39345 1uwkA 557 2.17e+01 e.51.1.1 108065 1dzoA 123 2.17e+01 1dzoA d.24.1.1 38378 1nzjA 298 2.21e+01 c.26.1.1 92377 2g1uA 155 2.32e+01 1kxgA 152 2.36e+01 b.22.1.1 73145 1j75A 67 2.38e+01 a.4.5.19 62673 1voqa 90 2.44e+01 1oixA 191 2.47e+01 1yk4A 52 2.49e+01 1g99A 408 2.52e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 2g6tA 306 2.54e+01 1j1nA 492 2.55e+01 c.94.1.1 83978 1sr8A 298 2.56e+01 e.54.1.1 105959 1e6yB 433 2.59e+01 1mroB a.89.1.1,d.58.31.2 18535,39453 1a7cA 379 2.68e+01 1sek e.1.1.1 42660 1rb9 53 2.73e+01 1rb9 g.41.5.1 45214 1sc6A 404 2.75e+01 1mo9A 523 2.75e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1ciy 590 2.84e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1qo0D 196 2.86e+01 1qo0D c.23.1.3 31125 2bx2L 517 2.88e+01 1hf2A 210 2.88e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 1m3yA 413 2.94e+01 b.121.2.3,b.121.2.3 78579,78580 1u3eM 174 3.13e+01 d.4.1.3,d.285.1.1 107640,107641 1m1eB 81 3.16e+01 a.161.1.1 78400 1zbpA 273 3.24e+01 1qfhA 212 3.25e+01 1qfhA b.1.18.10,b.1.18.10 21893,21894 1ltsA 185 3.34e+01 1lt3A d.166.1.1 42229 1ko3A 230 3.47e+01 d.157.1.1 90974 1tcrA 202 3.49e+01 1tcrA b.1.1.1,b.1.1.2 20605,21549 1oy3D 282 3.49e+01 d.211.1.1 87554 2bsaA 303 3.51e+01 1obdA 306 3.52e+01 d.143.1.1 86767 1i2aA 219 3.53e+01 e.24.1.1 90660 1owcA 427 3.55e+01 a.103.1.1 104039 1ogiA 303 3.56e+01 b.43.4.2,c.25.1.1 92914,92915 1gci 269 3.56e+01 1gci c.41.1.1 32503 1prxA 224 3.61e+01 1prxA c.47.1.10 33076 1oivA 191 3.63e+01 c.37.1.8 93076 1w34A 304 3.72e+01 1f9yA 158 3.74e+01 d.58.30.1 83249 1k3pA 426 3.74e+01 a.103.1.1 77237 1i60A 278 3.86e+01 c.1.15.4 71118 1tt8A 164 3.92e+01 1que 303 3.92e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1i8aA 189 3.99e+01 1i82A b.1.9.2 61951 1z7bA 358 3.99e+01 1fo8A 343 4.13e+01 1foaA c.68.1.10 59927 1yua 122 4.16e+01 1yua g.41.3.3,g.41.3.3 45210,45211 1p49A 562 4.18e+01 c.76.1.2 94089 1zwyA 185 4.20e+01 2fomB 185 4.22e+01 2alaA 391 4.26e+01 1x2iA 75 4.28e+01 1avyA 74 4.34e+01 1avyB h.1.17.1 45656 1zz1A 369 4.34e+01 2cx5A 158 4.35e+01 1gjwA 637 4.35e+01 b.71.1.1,c.1.8.1 60582,60583 1fw9A 164 4.41e+01 1fw9A d.190.1.1 60059 2f4mA 295 4.43e+01 1qi9A 556 4.55e+01 1qhbA a.111.1.2 19053 1qopB 396 4.56e+01 2tysB c.79.1.1 35270 1ak0 270 4.59e+01 1ak0 a.124.1.2 19345 2bgiA 272 4.59e+01 1dqqB 210 4.61e+01 1igtB b.1.1.1,b.1.1.2 20421,21391 1go2A 304 4.62e+01 b.43.4.2,c.25.1.1 76243,76244 4blmA 265 4.68e+01 1btl e.3.1.1 42721 1ypvA 313 4.70e+01 1tukA 67 4.72e+01 1cex 214 4.87e+01 1cex c.69.1.30 31285 1hynP 379 4.87e+01 1hynP d.112.1.2 61408 1t6kA 278 4.88e+01 1ukvY 206 4.95e+01 c.37.1.8 107918 2f6eA 127 4.97e+01 2gc9A 179 5.00e+01 2b0aA 186 5.04e+01 1iq9A 61 5.11e+01 g.7.1.1 90669 1g79A 218 5.14e+01 1ci0A b.45.1.1 25752 1yqfA 203 5.14e+01 1w4xA 542 5.16e+01 c.3.1.5,c.3.1.5 109171,109172 1ffa 214 5.16e+01 1cex c.69.1.30 31289 1idrA 136 5.20e+01 1dlyA a.1.1.1 62301 1u6zA 513 5.20e+01 1wlnA 120 5.26e+01 2bcgY 206 5.27e+01 1f00I 282 5.35e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1pdkB 157 5.41e+01 1pdkB b.2.3.2 22427 1iw7C 1119 5.43e+01 e.29.1.1 71474 1budA 197 5.44e+01 1atlA d.92.1.9 40328 1u9jA 358 5.49e+01 1rerA 391 5.49e+01 b.1.18.4,f.10.1.1 97327,97328 1e79G 272 5.52e+01 1e79G c.49.2.1 33158 2f9lA 199 5.60e+01 2bllA 345 5.60e+01 1yp2A 451 5.63e+01 2ae0X 345 5.67e+01 1z2aA 168 5.73e+01 1brfA 53 5.74e+01 1rb9 g.41.5.1 45236 1xg7A 250 5.85e+01 1bk0 331 5.86e+01 1bk0 b.82.2.1 28118 1grj 158 5.92e+01 1grj a.2.1.1,d.26.1.2 15691,38433 2ck3G 272 5.95e+01 1bq9A 54 5.97e+01 1rb9 g.41.5.1 45238 1ngkA 128 6.01e+01 a.1.1.1 85673 2gf9A 189 6.03e+01 2sak 121 6.06e+01 2sak d.15.5.1 37711 1wzlA 585 6.06e+01 1odmA 331 6.07e+01 b.82.2.1 86875 1y43A 39 6.08e+01 1ta8A 332 6.08e+01 2flsA 132 6.11e+01 1u58A 253 6.14e+01 1mroB 442 6.15e+01 1mroB a.89.1.1,d.58.31.2 18531,39449 1mr7A 209 6.49e+01 b.81.1.3 91430 1w6sA 599 6.52e+01 1fk5A 93 6.54e+01 1rzl a.52.1.1 59866 1sffA 426 6.55e+01 c.67.1.4 105482 1vkmA 297 6.58e+01 c.138.1.1 108670 1lrwA 600 6.60e+01 b.70.1.1 91111 1wbpA 397 6.65e+01 1mzm 93 6.66e+01 1rzl a.52.1.1 17814 2bh9A 489 6.67e+01 1o91A 178 6.80e+01 b.22.1.1 92656 1zn6A 227 6.81e+01 1gpiA 431 6.87e+01 b.29.1.10 65450 1u8zA 168 6.89e+01 1zgoA 223 6.91e+01 1ouoA 210 6.93e+01 d.4.1.6 93554 1eqjA 511 6.98e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1js8A 394 7.04e+01 a.86.1.1,b.112.1.1 67219,67220 1u9tA 354 7.08e+01 2g1lA 104 7.09e+01 1h21A 247 7.12e+01 a.138.1.3 76510 1a12A 413 7.16e+01 1a12A b.69.5.1 27663 1r6dA 337 7.17e+01 c.2.1.2 97148 1vlqA 337 7.20e+01 c.69.1.25 108848 1o5zA 442 7.20e+01 c.59.1.2,c.72.2.2 92530,92531 1k7jA 206 7.22e+01 d.115.1.1 72103 2pil 159 7.22e+01 2pil d.24.1.1 38376 1rpa 342 7.24e+01 1cviA c.60.1.2 33983 1i58A 189 7.26e+01 1b3qA d.122.1.3 61773 1on2A 142 7.29e+01 a.4.5.24,a.76.1.1 87103,87104 12asA 330 7.30e+01 12asA d.104.1.1 40783 1hbnB 442 7.34e+01 1mroB a.89.1.1,d.58.31.2 60900,60901 2gaeA 346 7.36e+01 1b9oA 123 7.38e+01 3lzt d.2.1.2 36597 1eqoA 158 7.40e+01 1hka 1eur 365 7.41e+01 1eut b.68.1.1 27607 1eijA 80 7.43e+01 1eijA a.5.6.1 16298 1i2sA 282 7.43e+01 e.3.1.1 71104 2cxkA 95 7.45e+01 1mgrA 99 7.51e+01 d.1.1.2 79106 1vefA 395 7.54e+01 1pqzA 238 7.55e+01 b.1.1.2,d.19.1.1 104297,104298 2bmoA 447 7.64e+01 1fyhB 229 7.68e+01 1jrhI b.1.2.1,b.1.2.1 22055,22056 1s7jA 262 7.69e+01 d.21.1.2 98647 2fo3A 125 7.74e+01 2adgA 214 7.82e+01 2a8yA 270 7.86e+01 1mixA 206 7.89e+01 a.11.2.1,b.55.1.5 79166,79167 1nzyA 269 7.91e+01 1nzyA c.14.1.3 30903 1lkkA 105 7.94e+01 1lckA d.93.1.1 40412 1p7gA 222 7.95e+01 a.2.11.1,d.44.1.1 94223,94224 1c7kA 132 7.97e+01 1kuh d.92.1.1 59078 1pxfA 111 7.98e+01 b.40.4.4 88341 2calA 154 8.01e+01 1hcl 298 8.02e+01 1hcl d.144.1.7 41593 1ll7A 392 8.04e+01 c.1.8.5,d.26.3.1 78085,78086 1byrA 155 8.08e+01 1byrA d.136.1.1 41450 1y60A 169 8.11e+01 1dkzA 219 8.11e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1ghj 79 8.11e+01 1ghj b.84.1.1 28232 1d2kA 392 8.14e+01 1d2kA c.1.8.5,d.26.3.1 29008,38442 1j2jB 45 8.18e+01 a.7.8.1 84017 1xubA 298 8.21e+01 1lci 550 8.29e+01 1lci e.23.1.1 43349 1k3iA 656 8.32e+01 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 1y7wA 291 8.36e+01 1uisA 231 8.36e+01 d.22.1.1 99431 1ttwA 138 8.50e+01 d.198.1.1 107308 1kuh 132 8.58e+01 1kuh d.92.1.1 40258 1tns 76 8.66e+01 1qpmA a.6.1.7 16228 1jv4A 162 8.66e+01 b.60.1.1 67343 1of4A 179 8.69e+01 b.18.1.18 86932 2acjA 66 8.71e+01 2audA 257 8.86e+01 2dddA 225 8.89e+01 1rdg 53 8.89e+01 1rb9 g.41.5.1 45221 1h8eG 272 8.98e+01 1e79G c.49.2.1 60756